Parallelization of the molecular dynamics code GROMOS87 for distributed memory parallel architectures

DG Green*, KE Meacham, F vanHoesel

*Corresponding author for this work

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    4 Citations (Scopus)

    Abstract

    This paper describes the techniques and methodologies employed during parallelization of the Molecular Dynamics (MD) code GROMOS87, with the specific requirement that the program run efficiently on a range of distributed-memory parallel platforms. We discuss the preliminary results of our parallel port and indicate to what extent we are able to satisfy the basic requirements of industrial users with regard to code performance and scalability. We introduce a scheme which is used to dynamically allocate charge groups to processors reducing the time imbalance during the non-bonded force calculation phase from 30 - 40% to <1%. We propose a new method for parallelizing the constraint dynamics algorithm (SHAKE) where the emphasis is placed on reducing the number and size of communicated packets during the iterative SHAKEing process.

    Original languageEnglish
    Title of host publicationHIGH-PERFORMANCE COMPUTING AND NETWORKING
    EditorsB Hertzberger, G Serazzi
    Place of PublicationBERLIN 33
    PublisherSpringer
    Pages875-879
    Number of pages5
    ISBN (Print)3-540-59393-4
    Publication statusPublished - 1995
    EventInternational Conference and Exhibition on High-Performance Computing and Networking - , Italy
    Duration: 3-May-19955-May-1995

    Publication series

    NameLECTURE NOTES IN COMPUTER SCIENCE
    PublisherSPRINGER-VERLAG BERLIN
    Volume919
    ISSN (Print)0302-9743

    Other

    OtherInternational Conference and Exhibition on High-Performance Computing and Networking
    CountryItaly
    Period03/05/199505/05/1995

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